I think I've listed my favorites before in another old thread, but since a lot of things have changed since then I might as well post my new list here:
1. Koi Kaze (not for everyone, romantic slice-of-life drama with a serious incest theme)
2. TEXHNOLYZE (not many people have seen this one but it's an absolutely awesome cyberpunk series!)
3. Serial Experiments Lain (also cyberpunk)
4. NGE
5. Kino no Tabi
6. Gunslinger Girl
7. Saikano
Gungrave was also pretty good, but most of Brandon's gunfights just looked ridiculous and I couldn't help but feel bored sometimes while watching this. There are a few striking similarities with Berserk though, especially the relationship between Harry and Brandon felt very similar to the one between Griffith and Guts.